Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate 6938989 Sama_3087 ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:A0A159ZWL6 (233 letters) >FitnessBrowser__SB2B:6938989 Length = 243 Score = 127 bits (319), Expect = 2e-34 Identities = 77/237 (32%), Positives = 133/237 (56%), Gaps = 10/237 (4%) Query: 2 LQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRYM 61 L+ N++ Y Q + +V++ V G++V L+G NGAGK+T + G Q+ GSI Sbjct: 6 LKASNLAKSYKNRQVVKNVSLTVNTGQVVGLLGPNGAGKTTTFYMVVGLVQSDKGSIHIN 65 Query: 62 GEELVGQDSSHIM-RKSIAVVPEGRRVFARLTVEENLAM-----GGFFTDKGDYQEQMDK 115 ++L D H+ RK I +P+ +F +L+V +N+ TD + +E +++ Sbjct: 66 DDDLT-LDPMHLRARKGIGYLPQEASIFRKLSVRDNIMAVLQMRKELNTD--EREEALEQ 122 Query: 116 VLHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDI 175 +L F R G ++SGGE++ + I RAL + P+ +LLDEP G+ PI + I I Sbjct: 123 LLEEFHITHIR-DNLGMSLSGGERRRVEIARALAANPRFILLDEPFAGVDPISVIDIKKI 181 Query: 176 IEQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232 IEQL+ G+ V + + N + L + ++AY++ +G ++ +GT +L + +VR YLG Sbjct: 182 IEQLKNRGLGVLITDHNVRETLDVCEKAYIVSHGDLIAEGTPAEILDNQQVRAVYLG 238 Lambda K H 0.320 0.137 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 122 Number of extensions: 7 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 233 Length of database: 243 Length adjustment: 23 Effective length of query: 210 Effective length of database: 220 Effective search space: 46200 Effective search space used: 46200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory